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The SAM3U device has a ROM-resident bootloader. This means the bootloader is always present - unless the chip is damaged it can be run, making the device almost "unbrickable". If you have trouble running the instructions on this webpage it's most likely an issue with your host computer, and not an issue with the SAM3U being damaged.
==Entering Bootloader Mode==
If using Linux, you can use ''dmesg'' to verify the serial port was connected OK.
==Flashing Firmware Using BOSSA==
The suggested utility to program the device is BOSSA - see [http://www.shumatech.com/web/products/bossa] for details. Before proceeding, install BOSSA for your system.
Run BOSSA, and in the "File" point it to chipwhisperer\hardware\capture\chipwhisperer-lite\sam3u_fw\SAM3U_VendorExample\Debug\SAM3U_CW1173.bin from either your release or GIT. If you press the "Auto-Scan" button BOSSA should detect the ATSAM3U2 device. Note if you are using Windows it might take a few minutes to install the drivers - check the status, as until the drivers are fully loaded it won't detect the SAM3U device.
# Once this is done, press the Write button.
# Press Verify afterwards to confirm things worked.
# Press Exit to close out the program.
# Unplug & Replug the Micro-USB and you've got a working ChipWhisperer-Lite again, with the latest SAM3U firmware!
==BOSSA Command Line==